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- PDB-4fg6: Structure of EcCLC E148A mutant in Glutamate -

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Basic information

Entry
Database: PDB / ID: 4fg6
TitleStructure of EcCLC E148A mutant in Glutamate
Components
  • Fab fragment (Heavy chain)
  • Fab fragment (Light chain)
  • H(+)/Cl(-) exchange transporter ClcA
KeywordsTRANSPORT PROTEIN / transporter / Membrane
Function / homology
Function and homology information


cellular stress response to acidic pH / chloride:proton antiporter activity / voltage-gated chloride channel activity / proton transmembrane transport / chloride transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle ...Clc chloride channel / Clc chloride channel / Chloride channel, ClcA / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
H(+)/Cl(-) exchange transporter ClcA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.019 Å
AuthorsFeng, L. / MacKinnon, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular mechanism of proton transport in CLC Cl-/H+ exchange transporters.
Authors: Feng, L. / Campbell, E.B. / MacKinnon, R.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Nov 9, 2016Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_host_org_scientific_name / _software.classification ..._entity_src_gen.pdbx_host_org_scientific_name / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H(+)/Cl(-) exchange transporter ClcA
B: H(+)/Cl(-) exchange transporter ClcA
C: Fab fragment (Heavy chain)
D: Fab fragment (Light chain)
E: Fab fragment (Heavy chain)
F: Fab fragment (Light chain)


Theoretical massNumber of molelcules
Total (without water)193,0246
Polymers193,0246
Non-polymers00
Water00
1
A: H(+)/Cl(-) exchange transporter ClcA
C: Fab fragment (Heavy chain)
D: Fab fragment (Light chain)


Theoretical massNumber of molelcules
Total (without water)96,5123
Polymers96,5123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: H(+)/Cl(-) exchange transporter ClcA
E: Fab fragment (Heavy chain)
F: Fab fragment (Light chain)


Theoretical massNumber of molelcules
Total (without water)96,5123
Polymers96,5123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-30 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.455, 121.284, 151.698
Angle α, β, γ (deg.)90.000, 128.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H(+)/Cl(-) exchange transporter ClcA / ClC-ec1


Mass: 49600.660 Da / Num. of mol.: 2 / Mutation: E148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: Ss046 / Gene: b0155, clcA, eriC, JW5012, SSON_0167, yadQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P37019
#2: Antibody Fab fragment (Heavy chain)


Mass: 23823.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab fragment (Light chain)


Mass: 23088.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG300, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03332 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 61443 / % possible obs: 99.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.18 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.112.60.4561610.977199.9
3.11-3.232.60.30960881.029199.9
3.23-3.382.60.21761571.142199.9
3.38-3.562.60.14961531.241100
3.56-3.782.60.11261431.2061100
3.78-4.072.60.08661331.2661100
4.07-4.482.60.06561691.2651100
4.48-5.132.60.05861661.3161100
5.13-6.462.60.0561981.086199.9
6.46-502.50.03460751.274196.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTT

1ott


Resolution: 3.019→49.551 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 1.36 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 3060 4.98 %
Rwork0.2371 --
obs0.2389 61412 98.8 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.47 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 160.15 Å2 / Biso mean: 97.0865 Å2 / Biso min: 55.33 Å2
Baniso -1Baniso -2Baniso -3
1--4.8975 Å20 Å21.8307 Å2
2--40.1885 Å20 Å2
3----35.291 Å2
Refinement stepCycle: LAST / Resolution: 3.019→49.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13158 0 0 0 13158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713483
X-RAY DIFFRACTIONf_angle_d1.2518353
X-RAY DIFFRACTIONf_chiral_restr0.0792121
X-RAY DIFFRACTIONf_plane_restr0.0092302
X-RAY DIFFRACTIONf_dihedral_angle_d12.74722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0189-3.06610.36151130.36452227234083
3.0661-3.11640.40161340.354426432777100
3.1164-3.17010.39661530.345226762829100
3.1701-3.22770.34161320.318426942826100
3.2277-3.28980.33461430.306726602803100
3.2898-3.35690.37321210.31126662787100
3.3569-3.42990.30931580.287826562814100
3.4299-3.50970.33281320.283426772809100
3.5097-3.59740.28851510.271426632814100
3.5974-3.69470.35281350.264226632798100
3.6947-3.80330.28571250.266927172842100
3.8033-3.92610.28421550.251426482803100
3.9261-4.06630.32021370.238526852822100
4.0663-4.2290.26911460.230626762822100
4.229-4.42140.24721240.204526902814100
4.4214-4.65430.22221760.210726702846100
4.6543-4.94570.24111460.202726512797100
4.9457-5.32720.26921350.214727072842100
5.3272-5.86250.26981400.218327042844100
5.8625-6.7090.23931340.22727092843100
6.709-8.44590.19231280.185127332861100
8.4459-49.5580.26851420.22462537267992

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